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What it does:
Instead of determining your rare SNPs by sending your 23andMe results out to the internet, you can download this much smaller program to your computer. Currently it will only search for alleles with a prevalence rate of 1% or below.
It takes 30-60 seconds to run, completely with status bar and a display of your results as it finds them. Then you can save the results as a text file (tab separated) and/or .pdf file with nicely aligned columns and such. The results display allows you to move and sort the columns prior to generating the pdf file.
Homozygous results are flagged, and 23andMe "i" numbers are translated to "rs" numbers in the "ETC" column, when possible. Additional rs numbers are also provided, when available.
Why you'd use it:
It provides useful information regarding very rare SNPs. As someone with a debilitating disease featuring a lot of malfunctioning, it is possible that this information can help in uncovering the sources of problems.
One way to do that is by looking up the SNPs and seeing if they're pathogenic. Homozygous results are the most likely to cause problems, though multiple heterozygous pathogenic mutations on different strands of the same gene is often very problematic as well.
Another way to use the rare allele information is by comparing it to the rare alleles present in other people with the same illness. This has been done somewhat at http://forums.phoenixrising.me/index.php?threads/rare-allele-data.23978/, but really we need data from a lot more people, and a better way to sort and display it.
How to use the program:
(First you need to have downloaded and unzipped your 23andMe results from https://www.23andme.com/you/download/)
REQUIRED
Java - if you don't have Java, it's available for free at http://java.com/en/.
DOWNLOAD
1) Go to https://sourceforge.net/projects/analyzemygenes/
2) Click the dark green "download" button near the top center of the page
3) Chose "Open with", and hit OK - download should be very fast 👍
4) Click on "Extract all files" near the top left
5) Select a folder to extract them to, where you can find the files easily again. I suggest using the same folder you have your 23andMe results stored in.
RUN
6) Go to the folder where you extracted the files
7) Double-click on the "Genes"
8) A grey box with three buttons appears. The top one should be green. If it isn't, click on it to navigate to whatever dodgy location you've put the "one_percent" file in.
9) Click on the orange middle box to select your 23andMe file.
10) Click the yellow "Analyze" button, and wait for it to finish. This takes 52 seconds on my newish but basic laptop.
SAVING (Optional)
11) From the "Analysis results" chart which has appeared, you can drag the columns to change their order, or click on the tops of the columns to sort them (first click low to high, second click high to low).
12) Click on the "Save as text" button near the top of the chart. This creates a tab-separated text file.
13) Click on the "Save as PDF" button near the top of the chart. This creates a nice looking PDF file which is ideal for printing or easy reading.
IMPORTING TO EXCEL (Optional)
14) After saving the results as text, open Excel.
15) From the menu in Excel, select "Open".
16) Click on the "All Excel Files" button in the lower right corner and select "Text files" instead.
17) Navigate to the folder where you saved your results as a text file, and select it.
18) In the Excel "Text Import Wizard" which pops up, choose "Delimited" then click "Next"
19) Select "Tab" only, then click "Finish"
Any feedback, questions, suggestions, etc, very much appreciated, especially if it helps make the instructions clearer!